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infercna

Infer Copy Number Alterations and Clonality in (Single-Cell) RNA-Seq Data

kelvinny

Kelvin's R package that holds wrapper functions for a number of work things

kor_hcc

ktplots

Some tools for plotting single-cell data

leader_et_al

leukemia-paper

Analysis code and data for leukemia paper (preliminary title: Single cell mRNA signals reveal a distinct developmental state of KMT2A-rearranged infant B-lymphoblastic leukaemia)

luad_mirna_bayesianml

R code for synergetic LUAD miRNA signature analysis with Bayesian inference and machine learning approach

machine-learning-for-survival-ecml2020

Code repository for "A General Machine Learning Framework for Survival Analysis" published at ECML 2020

machine-learning-on-breast-cancer-survival-prediction

We used different machine learning approaches to build models for detecting and visualizing important prognostic indicators of breast cancer survival rate. This repository contains R source codes for 5 steps which are, model evaluation, Random Forest further modelling, variable importance, decision tree and survival analysis. These can be a pipeline for researcher who are interested to conduct studies on survival prediction of any type of cancers using multi model data.

machine_learning_excercises

Machine learning algorithms used for training

maier_et_al_nature_2020

This repository contains scripts used for analysis and figure generation in Maier, B., Leader, A.M., Chen, S.T. et al. A conserved dendritic-cell regulatory program limits antitumour immunity. Nature 580, 257–262 (2020). https://doi.org/10.1038/s41586-020-2134-y

mars

Discovering novel cell types across heterogenous single-cell experiments

master-thesis

metamarkers

Efficiently compute robust markers across single-cell datasets

metanet-analysis

Analysis and figure code from Jiang et al.

mlsurvival

Machine Learning for Survival Analysis

mmcp-counter

Murine version of MCP-counter, a tool to estimate the immune and stromal composition of heterogeneous tissue, from transcriptomic data

movics

Multi-Omics integration and VIsualization in Cancer Subtyping

multisurv

Multimodal deep learning model for long-term cancer survival prediction

myseuratwrappers

My extensions for Seurat package

neo2is_iths

neoantigenml

This is an neoantigens filtering repository by machine learning method

nextflow-tutorial

Nextflow training material for introductory tutorial

nf-phdcourse21

Nextflow training material for CRG PhD course 2021

nmd-paper

A pan-cancer genome-wide analysis reveals tumour dependencies by induction of nonsense-mediated decay

paper-covid19

pegasus

personalizedhealthcare

Personalized Healthcare Lab for Survival Analysis

phenograph

Subpopulation detection in high-dimensional single-cell data

pisces

R package for Protein activity analysis of single-cell RNAseq.